A method of controlling a continuously variable valve timing system, may include determining whether there is an error of a position of a cam, performing a passive control based on a value learned about a position of the cam during previous driving when it is determined that there is an error of the position of the cam, determining whether a motion of the continuously variable valve timing system is stopped while the passive control is performed based on the value learned about the position of the cam during the previous driving, learning the stopping position of the continuously variable valve timing system when it is determined that the motion of the continuously variable valve timing system is stopped, and learning a position for limp-home of the continuously variable valve timing system and then controlling the continuously variable valve timing system to the learned position for the limp-home.